Where is Vagrant saving changes to the VM?

Vagrant imports the base box which is located at ~/.vagrant.d/boxes/, like you said. This is where the base boxes are kept. It uses it to start a VM from the clean state. When importing a VM, the responsibility of where to store data files and VM state is up to VirtualBox itself. This is a configurable location but typically defaults to ~/VirtualBox\ VMS for Mac OS X and Linux. In Windows the boxes are kept in %userprofile%\.vagrant.d\boxes

It is easy to find the place where they are getting created, regardless of what platform you happen to be using.

1. Start VirtualBox. 
2. Go to the VM that shows as running instance. 
3. Check out the Settings ->Storage. 
4. You can find the path to location where VMs are created and stored in your file system.

I always change the directory that Virtualbox uses by default for VMs. Normally it is in your profile folder in Windows.

I change it to something like "D:\VHDs\VBox\" and there I found my vagrant test vm: "test01_1347456065". It was called test01, so I guess vagrant adds the numbers to keep things unique.